Windows 7 Recovery stuck at "Setup is Applying System Settings"?

I got a new Gateway computer for Christmas. I burned some recovery disks just in case. Today I downloaded a virus. When I opened the virus it disappeared out of the folder it was in and then I got the Blue Screen of Death. Great, right? Anyway, when I try to start the computer, it goes to the blue screen just as the desktop opens. I figured the virus just deleted some system files so I popped in the recovery disks and chose the option to back up all other files so that I wouldn't lose anything when I restored the system files. Now the computer seems to be hung at "Setup is applying system settings". Is there something wrong or does this process usually just take forever?